Yes VSEPR is only used for covalent bondings and that for ionic bonding, the shape is determined by crystal lattice packing theory.
You are right that BF3 is a covalent compound because of the very small size of boron compare to relatively large size of flourine. Imagine if they are packed in a crystal lattice, the relatively larger size of flourine will definitely cause a repelsion with each other, so the packing is not efficient at all. Therefore they would rather exist as molecule through covalent bonding.
As you might aware that there is hardly fully ionic or fully covalent, so there are things in between such as BF3 which is a polar covalent bond, as the covalent bond is polarize by the large difference in electronegativity.